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Unraveling Memory Formation: A Computational Model Reveals New Insights into Protein Structures at Synapses

Complex protein interactions at synapses are essential for memory formation in our brains, but the mechanisms behind these processes remain poorly understood. Now, researchers have developed a computational model revealing new insights into the unique droplet-inside-droplet structures that memory-related proteins form at synapses. They discovered that the shape characteristics of a memory-related protein are crucial for the formation of these structures, which could shed light on the nature of various neurological disorders.

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Memory formation is one of the brain’s most fundamental and complex functions, yet the microscopic mechanisms behind it remain poorly understood. Recent research has highlighted the importance of biochemical reactions occurring at postsynaptic densities – specialized areas where neurons connect and communicate. These tiny junctions between brain cells are now thought to be crucial sites where proteins need to organize in specific ways to facilitate learning and memory formation.

A 2021 study revealed that memory-related proteins can bind together to form droplet-like structures at postsynaptic densities, which scientists believe may be fundamental to how our brains create lasting memories. However, understanding exactly how and why such complex protein arrangements form has remained a significant challenge in neuroscience.

Against this backdrop, a research team led by Researcher Vikas Pandey from the International Center for Brain Science (ICBS), Fujita Health University, Japan, has developed an innovative computational model that reproduces these intricate protein structures. Their paper, published online in Cell Reports on April 07, 2025, explores the mechanisms behind the formation of multilayered protein condensates.

The researchers focused on four proteins found at synapses, with special attention to Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) – a protein particularly abundant in postsynaptic densities. Using computational modeling techniques, they simulated how these proteins interact and organize themselves under various conditions. Their model successfully reproduced the formation of the above-mentioned “droplet-inside-droplet” structures observed in earlier experiments.

Through simulations and detailed analyses of the physical forces and chemical interactions involved, the research team shed light on a process called liquid-liquid phase separation (LLPS); it involves proteins spontaneously organizing into condensates without membranes that sometimes resemble the organelles found inside cells. Crucially, the researchers found that the distinctive “droplet-inside-droplet” structure appears as a result of competitive binding between the proteins and is significantly influenced by the shape of CaMKII, specifically its high valency (number of binding sites) and short linker length.

These findings could pave the way toward a better understanding of the possible mechanisms of memory formation in humans. However, the long-term implications of this research extend well beyond basic neuroscience. Defects in synapse formation have been associated with numerous neurological and mental health conditions, including schizophrenia, autism spectrum disorders, Down syndrome, and Rett syndrome.

“Our results revealed new structure-function relationships between proteins at synapses,” said Dr. Pandey. “We hope that our findings will contribute to the development of novel therapeutic strategies for these devastating diseases.”

The project received funding from various organizations, including the Core Research for Evolutional Science and Technology (CREST), the Japan Science and Technology Agency (JST), JSPS KAKENHI, Kobayashi foundation, ISHIZUE2024 of Kyoto University, Grant-in-Aid for Scientific Research JP18H05434, and others.

References:

* Pandey, V., et al. (2025). Unraveling memory formation: A computational model reveals new insights into protein structures at synapses. Cell Reports.
* Japanese Ministry of Education, Culture, Sports, Science, and Technology (MEXT). (n.d.). Research Grants JP18H05434 and JP20K21462.

Asthma

Fatty Liver in Pregnancy Increases Risk of Preterm Birth, Study Finds

Pregnant women with metabolic dysfunction-associated steatotic liver disease (MASLD) have an increased risk of giving birth prematurely and the risk increase cannot be explained by obesity, according to a new study.

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Pregnant women who suffer from metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as non-alcoholic fatty liver disease, are more likely to give birth prematurely. A new study published in the journal eClinicalMedicine has found that these women have a significantly higher risk of preterm birth, and this increased risk cannot be attributed solely to their weight or obesity.

According to the research conducted by Karolinska Institutet, one in five people in Sweden may have MASLD, while globally, it could affect as many as three out of ten individuals. Common risk factors for developing the disease include metabolic disorders like type 2 diabetes and being overweight or obese. The study’s findings are based on Swedish registry data and included a total of 240 births among women with MASLD, along with 1140 matched births from the general population.

Alarmingly, the research revealed that women with MASLD were more than three times as likely to give birth prematurely compared to those without the disease. This increased risk persisted even after adjusting for factors such as weight and metabolic disorders. The study’s lead author suggests that this association may not solely be due to a high BMI, implying that the liver disease itself could have negative effects on pregnancy outcomes.

Moreover, women with MASLD had a 63 percent higher risk of caesarean section compared to the control group. However, this increased risk seemed to be explained by their high BMI, as no significant difference was observed when comparing them to overweight or obese women without fatty liver disease.

While the study’s findings are concerning, it is essential to note that MASLD itself did not increase the risk of congenital malformations in the children born to these women. The authors acknowledge that their research may have been influenced by other factors and emphasize the importance of closely monitoring pregnant women with MASLD to reduce the risk of complications.

The study’s conclusions highlight the need for specific recommendations regarding pregnancy care for women with MASLD, which could potentially be added to clinical guidelines for managing the disease.

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Animal Learning and Intelligence

Harnessing the Power of Nature: How Black Tea and Berries Can Promote Healthy Aging

Higher intakes of black tea, berries, citrus fruits and apples could help to promote healthy aging, new research has found.

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As we age, our bodies undergo various changes that can impact our physical and mental well-being. While some of these changes are inevitable, research suggests that incorporating certain foods into our diet can help promote healthy aging.

A recent study conducted by researchers from Edith Cowan University, Queen’s University Belfast, and Harvard T.H. Chan School of Public Health found that consuming higher intakes of black tea, berries, citrus fruits, and apples could lower the risk of key components of unhealthy aging, including frailty, impaired physical function, and poor mental health.

The study analyzed data from 62,743 women and 23,687 men over a period of 24 years. The findings revealed that women with the highest flavonoid intakes had a 15% lower risk of frailty, a 12% lower risk of impaired physical function, and a 12% lower risk of poor mental health compared to those with the lowest intakes.

While fewer associations were observed in men, higher flavonoid intake was still linked to a lower risk of poor mental health. The researchers suggested that regularly consuming flavonoid-rich foods could support healthier aging by reducing the risk of frailty, physical decline, and poor mental health.

The study’s lead author, Dr. Nicola Bondonno from Edith Cowan University, emphasized the importance of medical research in promoting healthy aging. “Our goal is not just to help people live longer but to ensure they stay healthy for as long as possible,” she said.

Professor Aedin Cassidy from Queen’s University Belfast added that flavonoids have been shown to reduce oxidative stress and inflammation, supporting blood vessel health, and even helping to maintain skeletal muscle mass – all of which are crucial for preventing frailty and maintaining physical function and mental health as we age.

The researchers noted that incorporating three servings of flavonoid-rich food into one’s diet could lead to a 6% to 11% lower risk across all three aging outcomes in females, and a 15% lower risk of poor mental health in males. This highlights the potential for simple dietary modifications to impact overall quality of life and contribute to the optimisation of healthy aging.

Overall, this study underscores the importance of incorporating flavonoid-rich foods into our diet to promote healthier aging. As Professor Eric Rimm from Harvard T.H. Chan School of Public Health noted, “These findings underscore the potential for simple dietary modifications to impact overall quality of life and contribute to the optimisation of healthy aging.”

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Cholesterol

Unlocking the Secrets of Human Longevity: A Decade of Discovery

Researchers participating in the Cilento Initiative on Aging Outcomes or CIAO study will gather in Acciaroli (Pollica-Cilento) Salerno, Italy to review a decade of work and plan their next steps. Launched in 2016, the CIAO study seeks to identify key factors (biological, psychological and social) that promote healthy aging and extreme longevity.

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The Cilento Initiative on Aging Outcomes (CIAO) study has been a decade in the making, and this month, researchers will gather in Acciaroli, Italy to review their progress and plan their next steps. Launched in 2016, the CIAO study seeks to identify key factors that promote healthy aging and extreme longevity.

The region of Cilento in southern Italy is home to a remarkable 300 residents who are over 100 years old and in robust health. This area was also the original source of research for Ancel Keys, the American physiologist who studied the influence of diet on health and promoted the benefits of the Mediterranean diet.

Scientists hope to reveal the longevity secrets of the Cilento region by using an array of tools to measure metabolomics, biomes, cognitive dysfunction, and protein biomarkers for risk of heart disease, Alzheimer’s, kidney disease, and cancer. They will also conduct psychological, social, and lifestyle surveys to gain a more comprehensive understanding.

“There is no single secret to living a long, healthy life,” said Salvatore Di Somma, MD, the study’s lead Italian investigator. “It is many secrets, most of which we are only beginning to understand and more importantly, learn how they might be applied to the well-being of everybody.”

The CIAO study is a multi-institution collaboration that includes Sanford Burnham Prebys, an independent nonprofit biomedical research institute in San Diego, the Sanford Stem Cell Institute at University of California San Diego, University La Sapienza in Rome, and Great Health Science.

A symposium will take place on May 22-23, featuring scientists describing their work and findings. The event is titled “CIAO Study: A decade of science on healthy aging, stem cells, and the revealed secrets of longevity.” Understanding how we age and how we might age better is a timeless pursuit, said David Brenner, MD, president and CEO of Sanford Burnham Prebys.

Current CIAO projects are leveraging genetic, epigenetic, transcriptomic, metabolic, proteomic, and environmental analyses to identify key contributors to extreme longevity. Researchers are using induced pluripotent stem cell (iPSC) derived from the centenarians to model age-related and metabolic stresses in human 3D organoids.

“This study will provide new insights into the development of regenerative medicine strategies for promoting healthy aging and treating age-related conditions,” said Tatiana Kisseleva, MD, PhD, professor of surgery at UC San Diego School of Medicine. Preliminary findings are expected to be presented at the symposium.

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